Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain

Varietal identification in pasta through an SSR-based approach: a case study

BACKGROUND

Pasta is a worldwide popular Italian food made exclusively of durum wheat. The choice of variety to be used to produce pasta is at the discretion of the producer based on the peculiar characteristics of each cultivar. The availability of analytical approaches for the tracking of specific varieties along the productive chain is becoming increasingly important to authenticate the pasta products and distinguish between fraudulent activities and cross-contaminations during the production process. Among the different methods, molecular approaches based on DNA markers are the most used for these purposes because of their ease of use and high reproducibility.

RESULTS

In the present study, we used an easy simple sequence repeats-based method to identify the durum wheat varieties used to produce 25 samples of semolina and commercial pasta comparing their molecular profile with those of the four varieties declared by the producer and other 10 durum wheat cultivars commonly used in pasta production. All of the samples showed the expected molecular profile; however, most of them present also a foreign allele indicating a possible cross-contamination. Moreover, we evaluated the accuracy of the proposed approach through the analysis of 27 hand-made mixtures with increasing amounts of a specific contaminant variety, allowing the estimation of the limit of detection of 5% (w/w).

CONCLUSION

We demonstrated the feasibility of the proposed method and its effectiveness in the detection of not declared varieties when these are present in a percentage equal to or higher than 5%. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Muscat Flavor in Grapevine: A Digital PCR Assay to Track Allelic Variation in VvDXS Gene

The aroma of grapes and derived wines has long been one of the major traits considered in the selection of grapevine varieties through the centuries. In particular, Muscat aromatic grapes have been highly appreciated and widespread since ancient times. Monoterpenes are the key compounds responsible for the Muscat flavor. A major QTL affecting monoterpene level has been found to co-localize with the 1-deoxy-D-xylulose 5-phosphate synthase (VvDXS) gene, encoding for the 1-deoxy-D-xylulose 5-phosphate synthase enzyme involved in the plastidial pathway of terpene biosynthesis. In more detail, a single nucleotide polymorphism (SNP 1822) in the coding region of the gene causes a "gain of function" mutation, which is involved in Muscat flavor. In this work, we have developed a digital PCR-based assay to target allelic variations in the VvDXS gene, SNP1822, with the aim to propose a fast and sensitive analytical tool for targeting Muscat-flavored grapevine genotypes. The assay accurately predicts the genetic structure at 1822 SNP, critical for the development of the aroma in the great majority of Muscats. In the case of grapes in which the aromatic component is due to mutations other than SNP 1822 (e.g., Chasselas Musqué and Chardonnay Muscat), further specific assays can be developed.